Thursday, January 31, 2013

This is a collection of Sandwalk posts on mutation starting in 2007. The latest ones are at the bottom of the list.

March 27, 2007Silent Mutations and Neutral Theory Neutral Theory and random genetic drift explains variation and it also explains molecular evolution and the (approximate) molecular clock. There are no other explanations that make sense and nobody has offered a competing explanation since Motoo Kimura (1968) or Jack King and Thomas Jukes (1969) published their papers almost fifty years ago. (Aside from occasional nitpicks, of course. There are always scientists who like to show that some mutations that were thought to be neutral are actually beneficial or deleterious. None of them have mounted a serious claim that most variation or most of molecular evolution can be explained by natural selection.)

April 19, 2007Haldane's DilemmaThis is very interesting. Dembski has teamed up with Walter ReMine, demonstrating once again that the old addage "opposites attract" does not apply to kooks.

ReMine has an article on Uncommon Descent where he pushes his usual whine about evil scientists and how their world-wide conspiracy has kept him from revealing the fatal flaw in evolution [Evolutionist withholds evidence on Haldane’s Dilemma]. I can see how similar this is to Intelligent Design Creationism.

Irony (from the Ancient Greek εἰρωνεία eirōneía, meaning dissimulation or feigned ignorance) is a rhetorical device, literary technique, or situation in which there is an incongruity between the literal and the implied meaning....

In dramatic irony, the author causes a character to speak or act erroneously, out of ignorance of some portion of the truth of which the audience is aware. In other words, the audience knows the character is making a mistake, even as the character is making it. This technique highlights the importance of a particular truth by portraying a person who is strikingly unaware of it.

The funny thing about irony (and sarcasm) is that there are so many people who are irony-deficient. They just don't get it. They seem to be incapable of recognizing anything other than the literal meaning of a statement. Look at the example given in the Wikipedia article (right figure). Then look at yesterday's Jesus and Mo cartoon (below). Both are excellent examples of intended irony.

Wednesday, January 30, 2013

This is pretty cool. You can ask Google Scholar to collect all citations to your published articles and display them as a chart [Citations]. I don't have a lot of citations but it's still fun to see them.

Allow me to lay my admittedly love-of-science, rant-tainted cards on the table. In general, the services provided by naturopaths reside either in the realm of commonsense lifestyle advice (get lots of sleep, eat well and stay active) or they have little empirical evidence to support their use. In fact, many naturopathic practices are based on a semi-spiritual theory (the healing power of nature), and have no foundation in science. They reside largely in the realm of pseudoscience.

Am I being too harsh? I recently worked with a University of Alberta colleague on an analysis of the websites for the naturopaths in Alberta and British Columbia. We wanted to get a sense of what is being offered to the public. In Alberta, the number one most commonly advertised service is homeopathy.

Homeopathy has been around for hundreds of years. The basic philosophy behind the practice is the idea of “like cures like.” A homeopathic remedy consists of a natural substance — a bit of herb, root, mineral, you get the idea — that “corresponds” to the ailment you wish to treat. The “active” agent is placed in water and then diluted to the point where it no longer exists in any physical sense.

In fact, practitioners of homeopathy believe that the more diluted a remedy is, the more powerful it is. So, if you subscribe to this particular worldview, ironically, you want your active agents to be not just non-existent, but super non-existent.

The bottom line: For those of us who reside in the material world, where the laws of physics have relevance, a homeopathic remedy is either nothing but water or, if in capsule form, a sugar pill.

There are people who don't live in the material world and they always pop out of the woodwork whenever their favorite superstitions are questioned. In this case, it's a homeopath named Karen Wehrstein who was given space on the newspaper website to respond to Timothy Caulfield [Homeopathy offers hope]. Wehrstein is described as ....

Karen Wehrstein is the executive director of the Canadian Consumers Centre for Homeopathy (homeocentre.ca), an organization formed in 2011 to educate the public about homeopathy and advocate for freedom of choice in health care.

Homeopathy’s big stumbling block to acceptance is that its medicines are diluted so much that people outside of the field can’t understand how they can possibly have an effect. There are, however many scientists who do have that expertise. So many, that there is an entire journal devoted to the field, the International Journal of High Dilution Research. And they seem to be getting intriguingly close to providing definitive answers.

Opponents of homeopathy claim that homeopathic medicines are “just plain water” with no medicinal properties. But increasing numbers of scientific findings are making it harder to maintain such as stance. One study has found that solutions prepared in the traditional homeopathic way — through repeated dilutions by mechanical shaking — have properties unlike plain water, with elements of the dissolved material. Another study suggests the solutions have an affect on living cells in vitro. Yet another study shows that solutions can be distinguished from each other, using the right equipment to determine their contents. And emerging research suggests that homeopathic solutions actually contain nanoparticles of the original dissolved material.

Students who have taken my course will recognize this kind of response. Science is so overwhelmingly respected these days that nobody can afford to be on the wrong side of scientific evidence. If you are defending quackery then you only have two choices; either you discredit the evidence against you or you make up scientific evidence to support your position. Most quacks do both. They end up simultaneously disparaging and praising scientists who work in the field.

Recent secular victories in Chilliwack are at risk.

On November 13th, the Board of the Chilliwack School District deleted Regulation 518 that stated, "The Board approves the distribution of Gideon Youth Testaments to Grade 5 pupils with parental consent." At the same meeting, the Board agreed to draft a new policy to permit the "distribution of materials" by March 2013.

This new policy represents an attempt to use public schools for religious proselytizing in BC public schools.

Superintendent Evelyn Novak intends to gather feedback through February to draft the new policy. While this feedback may not be open to the public, secular voices will be heard.

Please sign the petition below to send the message to the Chilliwack School Districts that BC schools should remain secular.

Sign the Petition. You will have to identify yourself but that shouldn't be a problem if you really believe in a secular school system.

Sunday, January 27, 2013

Last night the Liberal Party of Ontario selected a new leader, Kathleen Wynne. Since it's the governing party, she automatically becomes the Premier of Ontario.¹ I was hoping she would be chosen but in the last few weeks it looked like her opponent, Sandra Pupatello, was going to win.

Kathleen Wynne represents the leftish wing of the Liberal Party of Ontario and that's the view I support. Wynne becomes the first women Premier of Ontario and she joins five other women who lead provincial/territorial governments in Canada. As of today, almost 90% of Canadians live in provinces headed by a woman!

Kathleen Wynne is also the first openly gay person to head a provincial government. She is married to Jane Rounthwaite.² Her sexual orientation wasn't really much of an issue during the campaign. Here she is, thanking her partner Jane during the acceptance speech last night.

1. Subject to approval by the Lieutenant Governor.
2. Same-sex marriage has been legal in Ontario since 2002.

Friday, January 25, 2013

There are several types of genome sequence. Some are relatively incomplete and they don't really count. Others have been thoroughly sequenced and we have a good permanent draft sequence. The best ones are the "finished" genome sequences where the preliminary drafts have been checked and gaps have been filled.

How many "finished" or permanent draft complete genome sequences have been published?

Why are there so few eukaryotes? Because many eukaryotic genomes are very large and it takes a lot more work to sequence that much DNA. Furthermore, many eukaryotic genomes are full of junk DNA and it's difficult to sequence and assemble repetitive regions in order to get a complete chromosome. The bottom line is money—for most labs it's too expensive to sequence the genome of their favorite eukaryote but it can be quite cheap these days to sequence a bacterial genome.

Eric Lewellyn is an enthusiastic postdoc in the Drubin/Barnes Lab at US Berkeley. (They work on membrane trafficking.)

Eric tries to convince you to stay in university using song and dance. He describes all the good things about slaving away enjoying science in a research lab. I don't know Eric but I have met his mother—she's the cousin of one of our best friends.

I've long been a supporter of the Federal Liberal Party of Canada. It's the party of Mike Pearson and Pierre Elliot Trudeau—two Prime Ministers that I greatly admire. I even like Jean Chrétien!

Lately I'm having trouble understanding what the Liberal Party stands for. They've just had two leaders (Michael Ignatieff, and Bob Rae) who are complete mysteries to me. I really don't know what they stand for, or what they're passionate about.

On the other hand, it’s not clear what the Liberals represent any more. They would like voters to think of them as the non-Conservatives — the alternative to Stephen Harper federally or to Tim Hudak in Ontario.

But are they?

Paul Adams, an astute political observer writing in iPolitics, argues that the federal Liberals have transformed themselves into the old Progressive Conservatives, socially progressive but fiscally to the right.

Similarly, Liberal front-runner Justin Trudeau’s enthusiastic embrace of the Alberta oilsands would probably be seen as a tad naive by the Red Tories of former Ontario premier Bill Davis, most of whom believed that strong business required equally strong regulation.

As a party, the Liberals haven’t had a new idea since the 1980s. Individual party members have (Stéphane Dion’s green shift comes to mind).

But the party, as a whole never signed onto Dion’s environmental agenda. Nor has it signed onto anything else.

The Liberals talk of holding policy conventions that would replicate that golden period of the 1960s, when the party embraced medicare, public pensions and welfare reform.

But they never do. Former federal leader Michael Ignatieff hosted a thinkers’ conference that headlined prominent conservatives. Nothing came of it.

The conventional wisdom among Liberals is that strong policy positions should be avoided at all costs in order to avoid alienating voters. Instead, Liberals prefer to talk about what they call values.

We've been discussing this issue with our former Liberal MP, Omar Alghabra, who happens to be a member of Justin Trudeau's team. Justin, for those of you who don't follow Canadian politics, it the son of Pierre Elliot Trudeau and he's running for the leadership of the Federal Liberal Party. We want Justin, and all the other candidates, to speak out on what the Liberal Party stands for.

Omar sent us a link to this video. It's obvious that Justin is avoiding the question. He stands for some trivial issues like legalizing marijuana but what about the bigger issues? How do I tell the difference between the Liberal Party and Conservative Party or the New Democratic Party? I don't think I can vote for Justin Trudeau or for any of the other leadership candidates. In fact, I'm not sure I can vote for the Liberal in the next election. The NDP is looking very attractive.

Thursday, January 24, 2013

We had a fun meeting last night thanks to Rufina Kim [WTF Is Science?]. A bunch of students showed up along with Steve Livingston, the new co-Chair of CASS (Committee for the Advancement of Scientific Skepticism), and David Bailly, Chair of The Association for Science and Reason (Skeptics Canada).

Unfortunately we were not able to come to an agreement on "What Is Science."

Now we have to meet again in a couple of weeks!

We talked about whether there was a scientific method and whether falsifiability is part of the definition of science. The Wikipedia article on falsifiability is a good place to look for background information. Here are two sections from that article to get you started.

Paul Feyerabend examined the history of science with a more critical eye, and ultimately rejected any prescriptive methodology at all. He rejected Lakatos' argument for ad hoc hypothesis, arguing that science would not have progressed without making use of any and all available methods to support new theories. He rejected any reliance on a scientific method, along with any special authority for science that might derive from such a method. Rather, he claimed that if one is keen to have a universally valid methodological rule, epistemological anarchism or anything goes would be the only candidate. For Feyerabend, any special status that science might have derives from the social and physical value of the results of science rather than its method.

...

In their book Fashionable Nonsense (published in the UK as Intellectual Impostures) the physicists Alan Sokal and Jean Bricmont criticized falsifiability on the grounds that it does not accurately describe the way science really works. They argue that theories are used because of their successes, not because of the failures of other theories. Their discussion of Popper, falsifiability and the philosophy of science comes in a chapter entitled "Intermezzo," which contains an attempt to make clear their own views of what constitutes truth, in contrast with the extreme epistemological relativism of postmodernism.

Sokal and Bricmont write, "When a theory successfully withstands an attempt at falsification, a scientist will, quite naturally, consider the theory to be partially confirmed and will accord it a greater likelihood or a higher subjective probability. ... But Popper will have none of this: throughout his life he was a stubborn opponent of any idea of 'confirmation' of a theory, or even of its 'probability'. ... [but] the history of science teaches us that scientific theories come to be accepted above all because of their successes." (Sokal and Bricmont 1997, 62f)

They further argue that falsifiability cannot distinguish between astrology and astronomy, as both make technical predictions that are sometimes incorrect.

There's no such thing as a universal scientific method and falsifiability doesn't describe how the scientific way of knowing actually works.

I made up an example of a Professor of English whose research focuses on how the English language actually sounded in the time of Geoffrey Chaucer (about 1370)¹. Is she doing science? If not, what kind of way of knowing is she using?

1. This is roughly the time of World Without End. If the characters actually spoke in 14th century dialect we probably wouldn't have understood a word.

Wednesday, January 23, 2013

Think about that. In the early days of developmental biology, we didn’t even know whether there was differential gene activity or not; it was considered a reasonable possibility that all the genes were just doing their work, whatever it was, all the time in every cell, and that differences between cells emerged farther downstream, in biochemical interactions. But they knew this was an important question. They knew that we had to look at the activity of individual genes…they just didn’t have the tools yet. So it was back to hacking up embryos and trying to infer causes from aberrations.

The change emerged gradually, but there were a couple of watershed moments where everyone looked up and noticed that hey, we do have ways of looking at genes directly. One was the work of Ed Lewis, a most excellent geneticist who used the tools of genetics to look directly at mutations that caused changes in fly morphology, in the 1960s. This was amazing stuff — the papers he wrote were beautiful and complex and very, very genetical — but it was written in a language that most developmental biologists of the day were unprepared to read. They were genetics papers. But I think they laid a foundation: if you want to do development, you’d better learn about genetics.

The second big event was the saturation mutagenesis screen of Christiane Nusslein-Volhard and Eric Wieschaus, about 20 years later. This work was also built on an understanding of genetics, but also used the tools of molecular biology. It was another lesson: if you want to do development, you’d better learn about molecular biology.

I used to teach this stuff in the 1980s and I certainly agree with PZ that you need to understand molecular biology and gene expression.

When it came time to write my first textbook I incorporated the examples I had used in class. The first ones I described were: the early to late switch in gene expression in bacteriophage T4, sporulation in Bacillus subtilis, and the genetic switch in bacteriophage lambda. These were well-studied examples from experiments carried out in the 1970s. They teach fundamental concepts in developmental biology and they have an additional advantage; namely, they get students thinking about species that aren't animals.

These are still excellent examples that are well-understood at the molecular level. They are much easier to understand than Drosophila or plants. Unfortunately, we've educated an entire generation of developmental biologists who have never heard of these elegant examples.

Is this a good thing or a bad thing? Do students need to know the real history of developmental gene expression as worked out by scientists who studied phage and bacteria?

Here's a short paragraph containing three sentences from my textbook (page 584). Is there anything wrong with any of these sentences?

Under physiological conditions, double-stranded DNA is thermodynamically much more stable than the separated strands and that explains why the double-stranded form predominates in vivo. However, the structure of localized regions of the double helix can sometimes be disrupted by unwinding. Such disruption occurs during DNA replication, repair, recombination, and transcription.

Having trouble seeing where I went wrong, according to some people? Check out this and this.

Tuesday, January 22, 2013

Everyone knows about TED talks (Ideas Worth Spreading). They know that TED talks are "riveting talks by remarkable people." Or at least that's what they would like to believe [TED Tries to Clean Up Its Act].

Here's some worthy competition to TED talks from The Onion. It's title is Using Social Media To Cover For Lack Of Original Thought.

Monday, January 21, 2013

The last "Monday's Molecule" was 2R,3S-isocitre [Monday's Molecule #197]. The winner was Evey Salara. She's probably too far away to come for lunch.

This week's molecule is very strange looking but it serves a very important role in some species. What is the molecule, what species have it, and what does it do?

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

So far there are almost 200 votes and "EvoDevo" is leading the pack (Boo!). I'm delighted to see that "Nonadaptive Evolution of Complexity" is getting a substantial number of votes. It suggests that there are people who really do understand Michael Lynch and Eugene Koonin (among others).

"Epigenetics" is way too popular. It is NOT an addition to evolutionary theory, in my humble opinion.

Here are some definitions of science from the Oxford English dictionary.

The state or fact of knowing; knowledge or cognizance of something specified or implied; also, with wider reference, knowledge (more or less extensive) as a personal attribute.

Knowledge acquired by study; acquaintance with or mastery of any department of learning. Also +pl. (a person's) various kinds of knowledge.

A particular branch of knowledge or study; a recognized department of learning.

In a more restricted sense: A branch of study which is concerned either with a connected body of demonstrated truths or with observed facts systematically classified and more or less colligated by being brought under general laws, and which includes trustworthy methods for the discovery of new truth within its own domain.

The kind of knowledge or of intellectual activity of which the various `sciences' are examples. In early use, with reference to sense 3: What is taught in the schools or may be learned by study. In mod. use chiefly: The sciences (in sense 4) as distinguished from other departments of learning; scientific doctrine or investigation. Often with defining adj. as in 4 b.

Saturday, January 19, 2013

Have you ever heard anyone say that they don't need to get a vaccination because they never get the disease and, even if they do, it's never very serious?

That's fine if the only person you care about is you. Maybe you live in a cave. Maybe you never visit old people in a retirement home. Maybe you are never near babies. Maybe you don't have a spouse or a partner. (I can't imagine why such a self-centered person would not have a partner.)

Or maybe you just don't understand the concept of herd immunity. Ignorance can be cured ....

Thursday, January 17, 2013

If you live outside of the USA you may not have seen this television ad paid for by the National Rifle Association.

It's tantamount to a declaration of war on the issue of gun control. What this means is that there is no compromise or middle ground with these people. I hope Obama accepts the challenge and takes on the gun lobby. Last I heard, they were not a democratically elected part of the legislature.

BTW, if members of the NRA are really interested in protecting their children from the risk of being killed by guns then they should send them to school in the UK. Even Canada would be better.

Most eukaryotic genes have introns. Introns make up about 18% of the DNA sequences in our genome. Most of these sequences are junk but introns are functional and up to 80bp of each intron is required for proper splicing. The essential sequences contain the 5′ splice site (~10 bp); the 3′ splice site (~30 bp): the branch site (~10 bp); and enough additional RNA to form a loop (~30 bp). The branch site and the splice sites are where specific proteins bind to the mRNA precursor [Junk in Your Genome: Protein-Encoding Genes]. It turns out that within introns about 0.37% of the genome is essential and about 17% is junk.

You'd think that most of the responses would be along the lines of global climate change, poverty, disease, crime, war, or the possibility that Earth might be destroyed by an asteroid impact. You'd think that the treatment of women in third (and second) world countries and the fanaticism of religious extremists might generate more than a few responses.

You would be wrong.

Here's what the best minds in the Western world came up with. I read most of them and I don't think I'll lose any sleep over any of these worries. I will, however, continue to lose sleep over women being raped in India and young children being shot to death in Connecticut.

Chinese Eugenics
What We Learn From Firefighters
That We Won't Make Use Of The Error Catastrophe Threshold
A Fearful Asymmetry: The Worrying World Of A Would-Be 'Science'
Misplaced Worries
We Are In Denial About Catastrophic Risks
The Disconnect
Unfriendly Physics, Monsters From The Id, And Self-Organizing Collective Delusions
Worry About Internet Drivel
We Don't Do Politics
The Black Hole Of Finance
The Opinions Of Search Engines
The Mating Wars
Computer-Generated Fascism
Who's Afraid Of The Big Bad Words?
Data Disenfranchisement
The Patience Deficit
The Underpopulation Bomb
Big Experiments Won't Happen
"Smart"
What—Me Worry? by Craig Venter (one of the few decent responses)The Promise Of Catharsis
I've Given Up Asking Questions
The Anthropocebo Effect
The Relative Obscurity Of The Writings Of Édouard Glissant
The Danger Of Inadvertently Praising Zygomatic Arches
The Loss Of Death
One Universe
The Rise Of Anti-Intellectualism And The End Of Progress
Applying Classic Science To Understand "Modern States" Shaped By Crime
Lamplight Probabilities
What Is Conscious?
Men
Science By (Social) Media
Unmitigated Arrogance
Technology May Endanger Democracy
"The Singularity": There's No There There
MADness
Blown Opportunities
The Power Of Bad Incentives
Quantum Mechanics
Are We Homogenizing The Global View Of A Normal Mind?
Science Publishing
Is The New Public Sphere... Public?
World As We Know ItStress by Arianna Huffington, who is one of the important causes of stressScience Has Not Brought Us Closer To Understanding Cancer
Losing Touch
The Human-Nature Divide
Are We Becoming Too Connected?
Putting Our Anxieties To Work
Incompetent Systems
Too Much Coupling
Power And The Internet
Close To The Edge
The End Of Fundamental Science?
The Paradox Of Material Progress
The Fragility Of Complex Systems by Randolph Nesse, worth a readRats In A Spherical Trap
Close Observation And Description
Global Greying
The Fourth Culture
The Coming Fight Between Engineers And Druids
Impact
The Complex, Consequential, Not-So-Easy Decisions About Our Water Resources
Children Of Newton And Modernity
The Teenage Brain
Augmented Reality
Where Did You Get That Fact?
Social Media: The More Together, The More Alone
Is Idiocracy Looming?
The Disconnect Between News And Understanding
Objects Of Desire
Say It Ain't So
Being Told That Our Destiny Is Among The Stars
Global Cooperation Is Failing And We Don't Know Why
Morbid Anxiety
Worrying About Children
A Synthetic World
The Death Of Mathematics
Losing Our Hands
Internet Silos
The New Age Of Anxiety
Does The Human Species Have The Will To Survive?
All The T In China
Neural Data Privacy Rights
Armageddon
No Surprises From The LHC: No Worries For Theoretical Physics
Losing Completeness
Worries On The Mystery Of Worry
The Growing Gap Between The Scientific Elite And The Vast "Scientifically
Challenged" Majority
Presentism
Metaworry
Do We Understand The Dynamics Of Our Emerging Global Culture?
The Loss Of Lust
We Worry Too Much About Fictional Violence
The Consequences Of Our Increasing Knowledge Of What Causes Disease,
And Its Consequences For Human Freedom
Natural Death
C.P. Snow's 'Two Cultures': The Nature-Nurture Debate
The Demise Of The Scholar
The Unavoidable Intrusion Of Sociopolitical Forces Into Science
Who Gets to Play in the Science Ballpark
Communities Of Fate
Working with Others?
Working with Others?
Super-A.I.s Won't Rule The World (Unless They Get Culture First)
Posthuman Geography
The Danger From Aliens by Seth Shostak, way, way down on my listThe Role Of Microorganisms In Cancer Is Being Ignored By The Current Sequencing
Strategies
Human Intuitions Will Stifle Technological Progress
Illusions Of Understanding And The Loss Of Intellectual Humility
The End Of Hardship Inoculation
An Exploding Number Of New Illegal Drugs
Superstition by Matt Ridley, important but not in the top tenHistory And Contingency
The Triumph Of The Virtual, And Its Consequences
There Is Nothing To Worry About, And There Never Was
The Cultural And Cognitive Consequences Of Electronics
Failure Of Genomics For Mental Disorders
Crisis At The Foundations Of Physics
The Behavior Of Normal People
Democracy
Human Population, Prosperity Growth: One I Fear, One I Don't
Magic
The Rise In Genomic Instability by Eric J. Topol, gimme a break
Can They Read My Brain? by Stanislas Dehaene, who would want to?A World Without Growth?
The Dangerous Fascination Of Imagination
Worrying
The Gift Of Worry
Not Enough Robots
Safe Mode For The Internet?
Life As We Know I
Unknown Unknowns
Our Blindspots
The Is-Ought Fallacy Of Science And Morality
The Loss Of Our Collective Cognition And Awareness
The Decline Of The Scientific Hero by Roger Highfield, what's a
"scientific hero"?What Is A Good Life?
Digital Tat ...
Capture
Society's Parlous Inability To Reason About Uncertainty
Fast Knowledge
The "Nightmare Scenario" For Fundamental Physics
Homogenization Of The Human Experience
We Won't Be Able To Understand Everything by Clifford Pickover,
really? that worries you?Systematic Thinking About How We *Package* Our Worries
The Real Risk Factors For War by Steven Pinker, yes, we should be
worried about war
Worrying About Stupid
The Belief Or Lack Of Belief In Free Will Is Not A Scientific Matter
Science Is In Danger Of Becoming The Enemy Of Humankind
Living Without The Internet For A Couple Of Weeks by Daniel Dennett,
not in my top ten

There are millions and millions of atheists around the world. Whether it's in Brussels or Beijing these atheists cope with deaths in the family in a variety of ways. None of them require the false comfort of god(s) or heaven.

I live in a (relatively) secular society. Most of my friends are nonbelievers. We are at the age where the deaths of friends and family members are not uncommon. In many cases, the memorial services are completely non-religious but even in those cases where the service takes place in a church my friends are not troubled by their lack of belief in god(s).

However, problems arise in societies where the vast majority of people are religious and where the believers have no concept of what it might be like to be an atheist. The problems aren't caused by the inability to cope with death in the absence of god, they are caused by intolerant and insensitive believers who can't, or won't, recognize that their false beliefs provide no comfort to an atheist. That's why there's so much talk these days about how atheists cope with death in the USA [After Tragedy, Nonbelievers Find Other Ways To Cope].

If you read the examples in that article, you will realize that the problems they face would not exist in non-religious societies. Their "problems" all stem from feelings of guilt about not believing or from interfering Christians. You won't see articles like this published in Brussels or Beijing.

The video below, narrated by Jon Perry, answers the question, What Exactly Is Evolution. It starts with an excellent definition of evolution that closely resembles my own preferred, minimal, defintion of evolution at What Is Evolution?. Here's the definition in the video ...

(Evolution is defined as) any change in the heritable traits within a population across generations.

The first example involves a new mutation that arises in an amoeba-like organism. Because this new mutation in inherited by a daughter cell, the video declares that "evolution has officially occurred."

What this means is that mutation becomes a mechanism of evolution. I prefer to think of evolution as "heritable changes in a population spread over many generations" in order to make it clear that change in a single generation doesn't qualify. I also prefer to think of mutation as a mechanism for generating variation and not a mechanism for causing evolution but this can be legitimately debated.

The second example is two badgers mating to produce an offspring that has a different combination of characteristics than either parent. According to the video "evolution ... has officially occurred." This is incorrect. Populations evolve, not individuals. It's quite possible for the individuals in a given generation to have different combinations of traits than either of their parents while the frequency of alleles in the population remains unchanged. Thus, evolution has NOT occurred.

The idea that it's populations that evolve and not individuals is crucial to a correct understanding of evolution and it's a shame that the video promotes a common misconception.

Tuesday, January 15, 2013

Rufina is a student at the University of Toronto and she's interested in setting up a group/club to discuss science. Here's what she has in mind.

The goal of this group is to meet regularly (~biweekly) to discuss/debate the hot topics in scientific controversy and their implications in the sociopolitical world. My personal aim in founding this group is to refine the art of delivering articulate and diplomatic scientific explanations to those who don't "believe" in science. In addition, I would like to expand our efforts to somehow elucidating to the general public/non-science students the importance of science in the progress of society.

I'm in.

The first meeting will be Wednesday, January 1623, 2013 at 6pm at a location to be decided. (Probably in my building.) The topic of the first meeting is "What Is Science."

Monday, January 14, 2013

This is a BBC One program posted to YouTube on Jan. 13, 2013. The question is whether it's time for all regions to accept evolution. The answer is "yes" of course, but some religions are going to resist for a bit longer. Because this is Britain, it's not so much the Christians that are the problem but Muslims.

You will recognize some of the people on this program. Matt Ridley, for example, gives a pretty good answer to the question about whether there's a scientific debate about the fact of evolution. It's amusing to read the response of Cornelius Hunter who claims that everything Ridley says is a lie [Here is How Evolutionists Lie to the Public].

Hunter says,

That was such a dizzying flurry of big lies we, frankly, lost count. Those lies are so absurd, so unequivocally false, and spoken with such conviction, that the average person is sure to believe them.

Unfortunately such lies are the rule rather than the exception. This evolution propaganda segment was no mistake—it is unfortunately typical.

Of course one can make truthful arguments for evolution. And one can try to find scientific evidence to support it. It is not easy, but it can be done. But that is not what evolutionists do. They mandate evolution. They insist evolution is a fact in spite of the evidence. And that is a big lie.

I don't think we're ever going to succeed in teaching the Cornelius Hunter's of this world the difference between truth and lies but TV shows like this one are having an impact and I'm glad to see that some Muslims are willing to speak out.

Shows like this one were very rare in the 20th century. It's now become much more acceptable to challenge religious beliefs that conflict with science and I think that's because of outspoken atheists like Richard Dawkins, Daniel Dennett, Christopher Hitchens, and Sam Harris, along with many other so-called "New Atheists."

The last "Monday's Molecule" was β-D-mannopyranose, shown in boat and chair configurations [Monday's Molecule #196]. The winners were Bill Chaney, Dima Klenchin, and Bill Gunn. Bill Gunn should contact me if he is within range of Toronto.

Students often find it very difficult to distinguish between various stereoisomers. For example, many of you thought that the last molecule was glucose. This week's molecule should present a real challenge for most of you. It's a common molecule, present in all cells and it has a common name by which it is identified in most textbooks. However, the common name isn't good enough because there are several different conformations. The conformation shown in the figure is the only one that's synthesized in the normal reaction. Name this molecule using whatever conventions you have to employ to identify it correctly. [Hydrogen atoms are omitted for clarity. You should be able to infer their positions.]

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Friday, January 11, 2013

The students in my Molecular Evolution class have to read the Spandrels paper by next Tuesday.

Ryan Gregory explains why this 35-year-old paper is just as relevant and important today as it was when it was first presented in 1978 (published in 1979). Read aall about it at: The great wrinkled finger debate.

A group of skeptics have banded together to sue Shoppers Drug Mart for selling the homeopathic product Oscillococcinum. Watch the video on Think Again! TV produced by Centre for Inquiry, Canada. This is a class action lawsuit and anyone who has purchased Oscillococcinum from Shoppers Drug Mart may join the plaintiffs.

CFI is not a plaintiff but it has agreed to provide the court with "accurate scientific data on the efficacy and substance of the product."

University professors have a lot less stress than most of us. Unless they teach summer school, they are off between May and September and they enjoy long breaks during the school year, including a month over Christmas and New Year’s and another chunk of time in the spring. Even when school is in session they don’t spend too many hours in the classroom. For tenure-track professors, there is some pressure to publish books and articles, but deadlines are few. Working conditions tend to be cozy and civilized and there are minimal travel demands, except perhaps a non-mandatory conference or two. As for compensation, according to the Bureau of Labor Statistics, the median salary for professors is $62,000, not a huge amount of money but enough to live on, especially in a university town.

Another boon for professors: Universities are expected to add 305,700 adjunct and tenure-track professors by 2020, according to the BLS. All of those attributes land university professor in the number one slot on Careercast.com’s list of the least stressful jobs of 2013. The ranking comes from an annual best and worst jobs list that began in 1995 under the auspices of the Wall Street Journal.

Ironically, this article comes out just as some of my colleagues are getting the bad news about their grant applications. Those who weren't funded face the end of their research career while they are still in their 40s. It also comes out at a time when two of my colleagues are starting to think about their applications for tenure. If they are unsuccessful, they will be out of a job in their late 30s with a family to support.

None of my colleagues took a month off at Christmas and I can assure you that all of my colleagues are here for almost the entire summer running a lab full of graduate students, post-docs, technicians, and summer students. The stress of running what amounts to a small business and getting papers published on things that nobody else has ever discovered is a lot more than most people could stand.

Read to the end of the Forbes article to see how the author responds to the many comments she received. The real problem here is that a prominent journalist could actually believe what she wrote in the first place!

I love the comment from Thomas Epps ...

Given your comment above indicating that you realize the source of your article was poor at best. I think you should consider retracting this article. I know that I would be severely sanctioned for writing this type of article with such questionable sourcing in my academic job. If the same is not the case in your job, then clearly your career is not a terribly stressful one. Maybe, "web staff writer" should be on the top of the "least-stressful jobs" list?

No comment is necessary except to say that this man, Louie Giglio, was all set to deliver the benediction at Obama's upcoming inauguration until it was discovered that he hates homosexuals. For me, this video would have been enough to disqualify him.

Wednesday, January 09, 2013

The Board of Directors of the Centre for Inquiry, Canada has mailed out the following press release. Unfortunately, nothing has been posted on the website [The Centre for Inquiry].

The Board of Directors would like to thank Justin for launching CFI Canada, growing it from one location in Toronto to across the country in short order. There are few individuals who possess the dedication, passion and tenacity to accomplish this. Justin was instrumental in making CFI the premier voice for reason, secularism and skepticism in Canada. We were fortunate to have him. Justin leaves CFI in good hands with our National Director, Michael Payton, and our incredible branch leaders and volunteers who are committed to continuing our growth and influence.

Justin, we look forward to watching you make further positive and lasting contributions to society, as no doubt you will.

Board of Directors, Centre for Inquiry Canada

I'm delighted that The Board and Justin were able to reach agreement on a new direction for CFI and usher in a new era under new leadership. I agree with the Board that Justin did an excellent job of creating CFI Canada and leading it through its formative years. I was happy to work with Justin and support him during those early years of building an organization (see photo).

In the past year I've been very critical of the CFI Board of Directors because I think they mishandled the firings and re-hirings that took place in 2011 and 2012. This time I think they've done the right thing during recent negotiations. Congratulations to Kevin Smith (President) and all the Board members for working hard to ensure the future success of CFI.

The email announcement also contained a letter from Justin Trottier to the Freehthinker members of CRI. It begins ....

Special Note from Justin Trottier, Founding National Executive Director, Centre for Inquiry Canada

To My Fellow Freethinkers,

It is with mixed emotions that I take this opportunity to announce the upcoming end of my leadership role with CFI Canada. March 15, 2013 will mark the end of my full-time position as National Communications Director; however, I will consider, if I am asked, continuing in part time or other status until no later than July 31. I am immensely proud of the contributions I've made to the organization over the last six years and plan to continue as a volunteer and active participant in CFI events and initiatives, but now it is time to start making the transition from CFI and pursue other interests and employment.

It has been a pleasure working with so many amazing people to form a unique Canadian educational charity and expand it into a national voice for atheists, humanists and skeptics from coast to coast. Leading CFI as it came to establish itself as the most visible, active and professional freethought organization in Canada, with employees, infrastructure and a growing budget will stand as one of the most important and certainly, matchless accomplishments of my life.

Friday, January 04, 2013

Jerry Coyne has posted a video of a happy young antelope jumping up and down in a style called "pronking" or "stotting" [Antelope pronking].

If you're a certain type of evolutionary biologist you will immediately ask yourself what kind of selective advantage could have led to the fixation of stotting alleles in antelopes? Here's a list of possibilities that Jerry offers ...

It allows an animal to jump out of high grass to look for predators

The behavior startles the predator, giving the gazelle more time to escape

It’s an alarm signal (like bird alarm calls), alerting herd members that a predator is nearby. This would probably evolve only if herd members were closely related, so the behavior could evolve via kin selection (assuming it’s individually maldaptive, which isn’t proven).

It’s simply play behavior. But not only the young do it: adults pronk too when they’re chased by predators.

It’s a way, in young gazelles, of letting the mother know the baby has been disturbed. This may be one function, but doesn’t explain stotting in adults.

It confuses the predator. Presumably a herd of gazelle, all pronking, would puzzle a pursuing cheetah or wild dog, making it hard to pick out a given individual to chase. I don’t believe this for a second; predators aren’t that dumb, and in fact a predator would probably either learn to or evolve to concentrate on the stotting individuals because they might be easier to catch. (This “confusion” explanation was once used to explain zebra stripes: it might be hard to single out one zebra in a mass of fleeing stripey equids. But see my earlier post on another explanation for stripes.)

It’s a way to attract mates, possibly by showing how fit you are. Sage grouse in the western U.S. form “leks” in which males group together and jump up and down for hours (making loud noises at the same time) while the females watch from nearby. Invariably it is the males who jump the longest that are chosen as mates. Females want a fit father for several reasons. This doesn’t wash for gazelles since both sexes do it, and not in a sexual context.

This is a favored hypothesis: the “honest signal” theory. This posits that the behavior is saying to potential predators, “Don’t bother trying to catch me as I can bounce really high, so imagine how fast I could run if I wanted to!” In other words, the behavior deters the predator from attacking that individual.

This is the hypothesis I find most credible: stotting warns the predator that it has been seen, thus discouraging it from pursuing the stotting animal. (Predators like to sneak up on a prey, getting as close as possible before they’re detected.) That is, stotting evolved via individual selection. Remember that predators often don’t go after a whole pack of quadrupeds at once, but single out certain individuals—often young or weak ones—to pursue.

Here's another example of animals jumping up and down in a stylized manner. Surely there are specific alleles that make them behave this way? And the alleles must have become fixed in the Maasi population by natural selection. In other words, it has to be an adaptation, right?

Do you see what's happening? Some upstart British colony from the bottom half of the world is beating Canada! We can't let that happen. If you are Canadian get yourself over to Atheist Census right away. If you're from Australia you can get your vote counted at Atheist Census for Australians. (Agnostics need not apply.)

Unfortunately, much of the discussion surrounding the publication of ENCODE failed to focus on the usefulness of the catalogue and the techniques that built it. Instead, much of the debate centered on the failure to understand that transcription does not necessarily imply meaningful biological function. Cells are messy biological entities, with lots of gunk and goo floating around, so mistakes happen all the time. Many DNA sequences get translated into RNA, only to have the cell degrade that RNA. Much, perhaps most, of the DNA in our genomes—despite being occasionally transcribed, and thus recorded in ENCODE—is still functionless “junk DNA.” That is actually not surprising; it is in fact expected from evolutionary theory. Thanks to ENCODE, though, we should eventually learn which sequences are the junk and which are the gems of cell activity.

This is a very different take on the subject than that published by the editors of Science and the Intelligent Design Creationists.

Most of the article is just the reposting of an article by Casey Luskin but some anonymous editor has added ...

Editor's note: For the No. 1 slot among evolution-related news stories of 2012, this one was an easy pick. The publication of the ENCODE project results detonated what had been considered among the sturdiest defenses that Darwinian evolutionary theory could still fall back upon: "Junk DNA." Casey Luskin's initial reporting is featured below. See also our response to the ensuing controversy over ENCODE ("Why the Case for Junk DNA 2.0 Still Fails").

Normally I would make fun of the creationists for misunderstanding the real scientific results in the papers that were published last September but, in this case, there are lots of real scientists who fell into the same trap.

Science magazine (published by AAAS) was one of the major news sources that fell hook, line and sinker for the ENCODE/Nature publicity campaign last September [Science Writes Eulogy for Junk DNA]. It even published a laudatory three page profile of Ewan Birney, the man responsible for misrepresenting the ENCODE results as evidence that most of our genome is functional [Ewan Birney: Genomics' Big Talker].

I was somewhat apprehensive when I saw that the editors of Science had picked the ENCODE results as one of the top ten breakthroughs [Genomics Beyond Genes]. Would the editors continue to promote the idea that most of the human genome is functional?

Welcome to 2013 and to Carnival of Evolution #55, and Happy New Year to everyone from Genome Engineering. Have you made any New Year’s resolutions this year? Apart from the oft repeated ‘This year I will write my novel’, here are some of my New Year’s resolutions for 2013.

New Year’s Resolution number one: Deliver Carnival of Evolution on time

Okay – broken that one already – sorry. Hope it was worth waiting for. Now onto the rest.

There's no host yet for the next Carnival of Evolution (February, 2013). If you want to volunteer to next month or for March, April, or May, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission.

Wednesday, January 02, 2013

I'm sure you've heard that Americans need guns so they can overthrow the government whenever it infringes on their personal beliefs. Many Americans believe they have a "right" to commit treason whenever they feel like it and, furthermore, that "right" must be protected by allowing them to bear arms, including assault weapons.

Here's what could happen. This is an interview by Janet Parshall of Mathew Staver. Believe it or not, Mathew Staver is Dean of the School of Law at Liberty University. He is also the Chair and Founder of a right-wing extremest group called Liberty Counsel. Mat is worried that the Supreme Court of the United States—the ultimate source of what's legal and what's not—could actually allow same-sex couples to get married!!!!

The consequences would be devastating, according to the Dean of Law. He says,

This is the thing that revolutions literally are made of. This would be more devastating to our freedom, to our religious freedom, to the rights of pastors and their duty to be able to speak and to Christians around the country, then anything that the revolutionaries during the American Revolution even dreamed of facing. This would be the thing that revolutions are made of. This could split the country right in two. This could cause another civil war. I’m not talking about just people protesting in the streets, this could be that level because what would ultimately happen is a direct collision would immediately happen with pastors, with churches, with Christians, with Christian ministries, with other businesses, it would be an avalanche that would go across the country.

I'm sure it's a great comfort to most Americans that these people have the weapons they need to start another civil war over legalizing gay marriage.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

Disclaimer

Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.